Dynamics Simulations Of Aqueous Solutions Research Articles

Molecular Dynamics Simulation of the Reaction of Hydration of Formaldehyde Using a Potential Based on Solute−Solvent Interaction Energy Components

Molecular dynamics simulations of aqueous solutions at infinite dilution of the reaction of water with formaldehyde, H(2)O + H(2)CO --> H(2)C(OH)(2), were performed using Lennard-Jones 12-6-1 potentials to describe the solute-solvent interactions, and TIP3P to describe the water-water interactions. The Morokuma decomposition scheme of ab initio interaction energies at the SCF level and the dispersion component at MP2 level were used to reproduce the molecular parameters of the solute-water interaction potential. The results show that the functions that use the EX-PL-DIS-ES interaction model to describe the solvation of the reactant and product systems lead to good values of the reaction (DeltaG) and activation (DeltaG(#)) free energy as compared with those from using AMBER-derived parameters, and with the available theoretical and experimental data.

Coupling between hydration layer dynamics and unfolding kinetics of HP-36

We have performed atomistic molecular dynamics simulations of aqueous solutions of HP-36 at 300 K in its native state, as well as at high temperatures to explore the unfolding dynamics of the protein and its correlation with the motion of water around it. On increasing the temperature a partially unfolded molten globule state is formed where the smallest alpha helix (helix 2) unfolds into a coil. It is observed that the unfolding is initiated around the residue Phe-18 which shows a sharp displacement during unfolding. We have noticed that the unfolding of the protein affects the density of water near the protein surface. Besides, the dynamics of water in the protein hydration layer has been found to be strongly correlated with the time evolution of the unfolding process. We have introduced and calculated a displacement time correlation function to monitor the change in water motion relative to the protein backbone during unfolding. We find that the unfolding of helix 2 is associated with an increase in mobility of water around it as compared to water around the other two helices. We have also explored the microscopic aspects of secondary structure specific and site specific solvation dynamics of the protein. The calculations reveal that unfolding influences the solvation dynamics of the protein molecule in a heterogeneous manner depending on the location of the polar probe residues. This seems to be in agreement with recent experimental findings.

Ultrasonic Velocities, Densities, Viscosities, Electrical Conductivities, Raman Spectra, and Molecular Dynamics Simulations of Aqueous Solutions of Mg(OAc)2 and Mg(NO3)2: Hofmeister Effects and Ion Pair Formation

The ultrasonic velocities, densities, viscosities, and electrical conductivities of aqueous solutions of magnesium nitrate and magnesium acetate have been measured from dilute to saturation concentrations at 0 < or = t/degrees C < or = 50. The temperature derivative of the isentropic compressibility, kappa(s), became zero at 2.28 and 2.90 mol kg(-1) for Mg(OAc)2 and Mg(NO3)2 solutions, respectively, at 25 degrees C. The total hydration numbers of the dissolved ions were estimated to be, respectively, 24.3 and 19.2 at these concentrations. Differences in kappa(s) for various M2+ salts, using the present and literature data, correlated with reported M2+-OH2 bond lengths and to a lesser extent with cationic charge densities (ionic radii). The influence of anions on kappa(s) appears to follow the Hofmeister series and also correlates approximately with the anionic charge density. Substantial differences between Mg(OAc)2(aq) and Mg(NO3)2(aq) occur with respect to their structural relaxation times (derived from compressibility and viscosity data) and their electrical conductivities. These differences were attributed to a much greater ion association in Mg(OAc)2 solutions. Raman spectra recorded at 28 degrees C confirmed the presence of various types of contact ion pairs including mono- and bidentate complexes in Mg(OAc)2(aq). In Mg(NO3)2(aq), only noncontact ion pairs appear to be formed even at high concentrations. The experimental results are supported by molecular dynamics simulations, which also reveal the much stronger tendency of OAc- compared to NO3- to associate with Mg2+ in aqueous solutions. The simulations also allow an evaluation of the ion-ion and ion-water radial distribution functions and cumulative sums and provide a molecular picture of ion hydration in Mg(OAc)2(aq) and Mg(NO3)2(aq) at varying concentrations.

QM/MM simulations of polyols in aqueous solution

We present QM/MM molecular dynamics simulations of aqueous solutions of polyols. The solute is treated at the AM1 semiempirical level and the TIP3P potential is used for the water molecules. We focus our attention on the intramolecular/intermolecular hydrogen bond balance and try to analyse the role of water in the sweet taste mechanism of polyols.

Molecular dynamics simulation of aqueous solutions using interaction energy components: Application to the dielectric properties of the acetone–water system

Molecular dynamics simulation of aqueous solution of acetone was made using Lennard–Jones 12-6-1 potentials to describe the solute–solvent interactions and TIP4P to describe the water–water interactions. The Morokuma decomposition scheme and the ESIE solute atomic charges were used to reproduce the molecular parameters of the solute–water interaction potential. The results showed that the functions that use the EX-DIS-ES model improve the values of the dielectric properties, in particular, the dielectric constant and the dielectric relaxation time.

Molecular Determinants of Topoisomerase I Poisoning by Lamellarins: Comparison with Camptothecin and Structure−Activity Relationships

A series of lamellarin derivatives have been studied as topoisomerase I (Top1) inhibitors. Molecular models of the ternary complexes formed between the DNA-Top1 ensemble and lamellarin D (LMD) or camptothecin (CPT) fully intercalated into the duplex DNA have been built and studied by means of nanosecond molecular dynamics simulations in aqueous solution. Our results show that the 20-OH and 8-OH of LMD can participate in hydrogen-bonding interactions with the side chains of Glu356 and Asn722, respectively, the latter being consistent with the finding that CEM/C2 cells, which are resistant to CPT, are cross-resistant to LMD. Our models also account for the observation that LMD stabilizes Top1 cleavage at CG sites in addition to the TG sites observed for CPT and rationalize the structure-activity relationships within the series. The deleterious effect of replacing the 20-OH in LMD with a hydrogen was confirmed using a set of thermodynamic integration free energy simulations.

Theoretical–experimental study of the solvation enthalpy of acetone in dilute aqueous solution

The present paper describes molecular dynamics simulations of aqueous solutions at infinite dilution with acetone as solute. Lennard-Jones with electrostatic term (12-6-1 potentials) were employed to describe the solute–solvent interactions. The Morokuma decomposition scheme of ab initio interaction energies at the SCF level and the ESIE charges on the solute atoms were used to reproduce the exchange and Coulomb electrostatic contributions of the solute–water interaction potential. Some extensions, such as including the dispersion component evaluated at MP2 level, were added to the traditional calculation procedures in order to improve the results of the solvation enthalpy. The results obtained with the EX–DIS–ES model were compared with the experimental calorimetry values, the observed agreement being acceptable.

Molecular Dynamics Simulation of Aqueous Solutions Using Interaction Energy Components: Application to the Solvation Gibbs Energy

Molecular dynamics simulations of aqueous solutions of the solutes acetamide (AcNH2), acetic acid (AcOH), and acetaldehyde (AcH) were made using Lennard–Jones 12-6-1 potentials to describe the solute–solvent interactions. The Morokuma decomposition scheme and the ESIE solute atomic charges were used to reproduce the exchange, polarization, and electrostatic components of the solute–water interaction energy. A nonlinear perturbation was incorporated into the “slow-growth” technique in order to improve the results for the solvation Gibbs energy that were found to be in agreement with the available experimental and theoretical values.

Molecular Dynamics Simulation of Aqueous NaF and NaI Solutions near a Hydrophobic Surface

We present results from molecular dynamics simulation of aqueous solutions of alkali halide salts (NaI and NaF) at the interface with hydrophobic objects. The primary objective of this study is to investigate the structural properties of the salt solutions at the hydrophobic surface. An alkane crystal has been taken as the parent model for a hydrophobic surface. A hexagonal hole was created on it, which was half a nm deep and 2.5 nm wide. The density distributions of different species (water, anions, and cations) are studied as a function of distance from the surface. While iodide prefers the interface, the fluoride ions stay inside the bulk water region. The higher concentration of iodide ions at the interface drags sodium counterions to the interface. It also decreases the water density at the interface because of steric effects of the iodide ions. The number of contacts between the surface carbons and water decreases in the case of NaI solutions but is unchanged for NaF solutions. The orientation of the water-ion and the water-water hydrogen bond vector orientations near the interface is discussed in detail.

Computational study of hydrated phosphate anions

Abstract The interaction of PO 4 3− with water has been investigated by ab initio calculations. Geometry optimizations of the orthophosphate anion complex with one or two water molecules (PO 4 3−/H 2O) show that the most stable conformations have C 2v symmetry and symmetrical hydrogen bonds as part of one or two six-membered rings. Intermolecular potential functions and an intramolecular force field were derived from ab initio calculated energies. They were used in molecular dynamics simulations of aqueous solutions of K 3PO 4, K 2HPO 4 and KH 2PO 4. The simulations were performed in the NVT ensemble with systems consisting of one anion and about 500 water molecules. The main results of the simulations are a pronounced first hydration shell consisting of about 16 water molecules for orthophosphate and about 20 water molecules for mono- and dihydrogenphosphate and a partially ordered second hydration shell. The results are in good agreement with recent experimental data.

Theoretical Study of a New DNA Structure: The Antiparallel Hoogsteen Duplex

The structure of a new form of duplex DNA, the antiparallel Hoogsteen duplex, is studied in polyd(AT) sequences by means of state-of-the-art molecular dynamics simulations in aqueous solution. The structure, which was found to be stable in all of the simulations, has many similarities with the standard Watson-Crick duplex in terms of general structure, flexibility, and molecular recognition patterns. Accurate MM-PB/SA (and MM-GB/SA) analysis shows that the new structure has an effective energy similar to that of the B-type duplex, while it is slightly disfavored by intramolecular entropic considerations. Overall, MD simulations strongly suggest that the antiparallel Hoogsteen duplex is an accessible structure for a polyd(AT) sequence, which might compete under proper experimental conditions with normal B-DNA. MD simulations also suggest that chimeras containing Watson-Crick duplex and Hoogsteen antiparallel helices might coexist in a common structure, but with the differential characteristics of both type of structures preserved.

Thermodynamic and dielectric properties of aqueous solutions using ESIE charges to describe small solutes

Abstract The present paper describes molecular dynamics simulations of aqueous solutions with two solutes of different behaviour in water as formaldehyde and formamide. Lennard–Jones (12-6-1) type potentials obtained from ab initio MP2 level energies corrected with the superposition error basis set were employed to describe the solute–solvent interactions. The Coulomb interactions of these potentials were determined using several sets of solute atomic charges (in gas and solution phase), paying especial attention to the ESIE charges that reproduce the electrostatic component of the solute–water interaction energy. Some properties were evaluated to explain the effect of the solute on the thermodynamic ( U sol , U rel ,Δ H sol ), and dielectric ( e and τ ) response of the evolving medium. Small modifications to the traditional procedures were included in the calculations in order to improve the results.

Molecular dynamics simulation of aqueous solutions of trimethylamine-N-oxide and tert-butyl alcohol

In this work we have investigated hydration properties of aqueous solutions up to a solute molar fraction X2 = 0.125 of two isosteric molecules – the bioprotectant trimethylamine-N-oxide (TMAO) and the denaturant tert-butyl alcohol (TBA) – using molecular dynamics simulation at 298 K. Statistical analyses of the trajectories show in particular that as the solute concentration increases the number of the water molecules in the first hydration shell decreases uniformly for TMAO, while for TBA it decreases more rapidly in a concentration range where experiments indicate that TBA starts to self-aggregate. No appreciable solute segregation occurs for TMAO even in the most concentrated solution, where on the average each water molecule is shared by two solutes. This result parallels what has been recently found for glycine betaine, an organic osmolyte closely related to TMAO.

Molecular dynamics simulation of aqueous solutions of glycine betaine

Molecular dynamics simulation is used to investigate hydration properties of glycine betaine in a large range of solute concentrations. Statistical analyses of the system trajectories evidence microscopic details suggesting an interpretation of experimental results recently obtained for aqueous solutions of trimethylamine- N-oxide, a bioprotectant closely related to glycine betaine.

Concentration Dependence of Water Dynamics in Poly(Ethylene Oxide)/Water Solutions from Molecular Dynamics Simulations

We have performed molecular dynamics simulations of aqueous solutions of poly(ethylene oxide) (PEO) in order to investigate the influence of the polymer on water dynamics. Simulations were performed on 12 repeat unit CH3-capped PEO chains (530 Da) at 318 K covering a composition range (polymer weight fraction) from 0.17 to 1.0. The simulations employed an ab initio quantum-chemistry-based PEO/water and PEO/PEO force field together with the TIP4P (four-point transferable intermolecular potential) water model. Water translational and rotational diffusion were found to slow monotonically, whereas water−water and water-ether hydrogen bond lifetimes increased with increasing polymer concentration. The slowing of water dynamics in PEO/water solutions was associated with PEO−water interactions that are moderated in concentrated solutions by the formation of water clusters. Water translational motion could be ascribed to a combination of free water (water not involved with PEO hydration) that exhibited bulklike water dynamics and bound (hydrating water) whose motion was strongly correlated with that of the PEO molecule. Water rotational motion was found to be strongly correlated with translation motion and exhibited increasing anisotropy with increasing PEO concentration indicative of preferred rotation of the water molecules around their dipole moment vector. At high PEO concentration, water and ether oxygen atoms exhibited well pronounced subdiffusive behavior occurring on a picosecond time scale that disappears upon dilution. The characteristic length scale for the water subdiffusive behavior associated with water caging correlates well with nearest-neighbor ether oxygen−ether oxygen distance.

Molecular dynamics simulations of pressure effects on hydrophobic interactions.

We report results on the pressure effects on hydrophobic interactions obtained from molecular dynamics simulations of aqueous solutions of methanes in water. A wide range of pressures that is relevant to pressure denaturation of proteins is investigated. The characteristic features of water-mediated interactions between hydrophobic solutes are found to be pressure-dependent. In particular, with increasing pressure we find that (1) the solvent-separated configurations in the solute-solute potential of mean force (PMF) are stabilized with respect to the contact configurations; (2) the desolvation barrier increases monotonically with respect to both contact and solvent-separated configurations; (3) the locations of the minima and the barrier move toward shorter separations; and (4) pressure effects are considerably amplified for larger hydrophobic solutes. Together, these observations lend strong support to the picture of the pressure denaturation process proposed previously by Hummer et al. (Proc. Natl. Acad. Sci. U.S.A. 1998, 95, 1552): with increasing pressure, the transfer of water into protein interior becomes key to the pressure denaturation process, leading to the dissociation of close hydrophobic contacts and subsequent swelling of the hydrophobic protein interior through insertions of water molecules. The pressure dependence of the PMF between larger hydrophobic solutes shows that pressure effects on the interaction between hydrophobic amino acids may be considerably amplified compared to those on the methane-methane PMF.

Concentrated aqueous MgCl2 solutions. A computer simulation study of the solution structure and excess electron localisation

Molecular Dynamics simulations of aqueous solutions of magnesium chloride were performed. The concentration of the solutions ranged from 0.2 to 4.9 M. The structures of hydration shells of the ions and the topological properties of the ionic structures were analysed using RDFs, Voronoi tessellations, coordination numbers, etc. The regions of crystalline order were found in concentrated MgCl2 solutions. Cation-centered clusters were selected to study the electron localisation. Quantum calculations were performed on the DFT level using 6-31++G** basis set. The absorption spectra of the excess electron in MgCl2 solutions were calculated by two different methods: histograms of the LUMO-HOMO energies and the excited states energies obtained from the time-dependent DFT.

A Molecular Dynamics Simulation Study of Polymer Dynamics in Aqueous Poly(ethylene oxide) Solutions

We have performed molecular dynamics simulations of aqueous solutions of poly(ethylene oxide) (PEO) in order to investigate the influence of water on polymer dynamics as a function of solution composition. Simulations were performed on 12 repeat unit PEO chains (530 Da) at 318 K covering a composition range (polymer weight fraction wp) from 0.17 to 1.0. It was found that addition of a small amount of water to a PEO melt dramatically affects polymer dynamics on all length scales, leading to a maximum in relaxation times in the range wp = 0.78−0.90, with the greatest effect occurring for smaller length-scale motions. With further dilution relaxation times decreased dramatically, with the greatest effect occurring for the largest length-scale motions. Water slows the rate of conformational transitions in PEO compared to the melt, an effect that sets in rapidly with initial dilution and saturates at wp ≈ 0.5. Initial addition of water leads to an increase in the heterogeneity of the rate of conformational transitions, with a maximum in the range wp = 0.78−0.90, followed by a decrease in heterogeneity with further dilution. A maximum in the non-Gaussianity of PEO atom displacements was observed in the same composition range. On the segmental scale, water was found to engender a monotonic decrease in relaxation anisotropy and an increase in the efficacy of conformational transitions in effecting PEO segmental relaxation. Finally, water was found to first lead to a slight increase and then to a dramatic decrease in the longest relaxation times of the solution, including viscosity, with dilution.

Poly(gamma-glutamic acid) in aqueous solution: molecular dynamics simulations of 10- and 20-residue chains at different temperatures.

A series of molecular dynamics simulations in aqueous solution have been carried out in order to investigate the effects of the length of the peptide chain and the temperature on the helical conformation of un-ionized poly(gamma-D-glutamic acid). The results reveal that the helix is not stable for a small number of residues independent of the temperature. On the other hand, the temperature induces a conformational transition from the helical state to the random coil. Analysis of the energy of the whole system indicates that the helix is more stable than the random coil state by about 5 kcal/mol, even although the solvation potential energy is lower in the latter than in the former.

Force-field parametrization and molecular dynamics simulations of p-menthan-3,9-diols: a family of amphiphilic compounds derived from terpenoids.

A set of amphiphilic p-menthan-3,9-diols have been investigated by molecular dynamics simulations. These are four stereoisomers than can be specifically obtained from two terpenoids widely used in biorganic chemistry. For this purpose, the p-menthan-3,9-diols have been explicitly parametrized using both semiempirical and ab initio quantum mechanical calculations. The reliability of these parameters has been validated by predicting different molecular and thermodynamic properties. Molecular dynamics simulations in aqueous solution have been performed with the new parameters. The results provide useful insights about the conformational properties of this family of compounds and the formation of intra- and intermolecular hydrogen bonds.